I tried searching through your responses to a number of issues and came across this in issue #65:
SURVIVOR merge sample_files 1000 1 1 0 0 30 merged.vcf
Is this how you would recommend creating a multi-sample VCF after consensus calling? If so, wouldn't the "30" indicated filter out SVs < 30bp? Also, why is the option to take the strands of SVs into account not a yes (1) here? Wouldn't this provide more certainty that it is the same variant being merged?
I'd appreciate your thoughts on this as I'm trying to determine the best options to use.
Hi,
I would like to create a multi-sample VCF post-consensus calling. Is there a recommended one-liner for this as there is for consensus calling on your wiki page? https://github.com/fritzsedlazeck/SURVIVOR/wiki#consensus-calling-or-comparing-svs-across-samples
I tried searching through your responses to a number of issues and came across this in issue #65:
SURVIVOR merge sample_files 1000 1 1 0 0 30 merged.vcfIs this how you would recommend creating a multi-sample VCF after consensus calling? If so, wouldn't the "30" indicated filter out SVs < 30bp? Also, why is the option to take the strands of SVs into account not a yes (1) here? Wouldn't this provide more certainty that it is the same variant being merged?
I'd appreciate your thoughts on this as I'm trying to determine the best options to use.
Thanks, Ike